Remove unused imports (#415)(patch)

### Fixed
- Removed unused package imports

cg_lims/EPPs/files/hamilton/normalization_file.py

@@ -10,7 +10,7 @@
 from cg_lims import options
 from cg_lims.EPPs.files.hamilton.models import BarcodeFileRow
 from cg_lims.exceptions import LimsError, MissingUDFsError
-from cg_lims.files.manage_csv_files import build_csv, sort_csv, sort_csv_plate_and_tube
+from cg_lims.files.manage_csv_files import build_csv, sort_csv_plate_and_tube
 from cg_lims.get.artifacts import get_artifacts
 
 LOG = logging.getLogger(__name__)

cg_lims/EPPs/move/rerun_samples.py

@@ -5,7 +5,7 @@
 from typing import List
 
 import click
-from genologics.entities import Artifact, Process, Stage
+from genologics.entities import Artifact
 from genologics.lims import Lims
 
 from cg_lims import options

cg_lims/EPPs/udf/calculate/calculate_water_volume_rna.py

@@ -8,7 +8,7 @@
 import click
 from genologics.entities import Artifact
 
-from cg_lims.exceptions import InvalidValueError, LimsError, MissingUDFsError
+from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.get.artifacts import get_artifacts
 
 LOG = logging.getLogger(__name__)

cg_lims/EPPs/udf/copy/artifact_to_artifact.py

@@ -1,4 +1,4 @@
-from typing import List, Optional, Tuple, Iterator
+from typing import List, Optional, Tuple
 from genologics.entities import Artifact
 from genologics.lims import Lims
 

cg_lims/EPPs/udf/copy/artifact_to_sample.py

@@ -1,10 +1,7 @@
 #!/usr/bin/env python
-import logging
 import sys
 
 import click
-from genologics.entities import Process
-from genologics.lims import Lims
 
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingUDFsError

cg_lims/EPPs/udf/copy/original_well_to_sample.py

@@ -2,9 +2,6 @@
 import sys
 import click
 
-from typing import List
-from genologics.entities import Process, Artifact
-from genologics.lims import Lims
 
 from cg_lims import options
 from cg_lims.exceptions import LimsError, InvalidValueError

cg_lims/EPPs/udf/copy/process_to_sample.py

@@ -1,13 +1,9 @@
 #!/usr/bin/env python
-import logging
 import sys
 
 import click
-from genologics.entities import Process
-from genologics.lims import Lims
 
 from cg_lims import options
-from cg_lims.exceptions import LimsError, MissingUDFsError
 from cg_lims.get.samples import get_process_samples
 
 

cg_lims/EPPs/udf/copy/qc_to_sample.py

@@ -2,8 +2,6 @@
 import sys
 
 import click
-from genologics.entities import Process
-from genologics.lims import Lims
 
 from cg_lims import options
 from cg_lims.exceptions import LimsError, MissingUDFsError

cg_lims/EPPs/udf/set/set_method.py

@@ -2,15 +2,15 @@
 """
 import logging
 import sys
-from typing import List, Optional
+from typing import List
 
 import click
 
 import requests
 from genologics.entities import Process
 
 from cg_lims import options
-from cg_lims.exceptions import LimsError, MissingUDFsError, AtlasResponseFailedError
+from cg_lims.exceptions import LimsError, AtlasResponseFailedError
 
 LOG = logging.getLogger(__name__)
 

cg_lims/get/files.py

@@ -1,12 +1,10 @@
 import pathlib
-from pathlib import Path
 from typing import Optional
 
 from genologics.config import BASEURI
-from genologics.entities import Artifact, Process
+from genologics.entities import Artifact
 from genologics.lims import Lims
 
-from cg_lims.exceptions import FileError
 
 
 def get_log_content(lims: Lims, file_id: str) -> str:

cg_lims/models/api/master_steps/pool_samples_twist_v2.py

@@ -4,7 +4,7 @@
 from pydantic.v1 import Field, validator
 
 from cg_lims.models.api.master_steps.base_step import get_artifact_udf, get_artifact_name, BaseStep
-from cg_lims.get.artifacts import get_latest_analyte, get_artifacts
+from cg_lims.get.artifacts import get_latest_analyte
 
 
 class PoolsamplesforhybridizationTWIST(BaseStep):

cg_lims/objects.py

@@ -1,6 +1,6 @@
 """Base cg_lims calss definitions
 """
-from typing import Optional, List
+from typing import Optional
 
 from genologics.entities import Artifact, Sample, Process
 from genologics.lims import Lims
@@ -16,7 +16,6 @@
     get_latest_analyte,
 )
 import logging
-from statistics import mean
 
 LOG = logging.getLogger(__name__)
 

cg_lims/put/queue.py

@@ -1,9 +1,8 @@
 import logging
-import pathlib
 from typing import List
 
 from genologics.config import BASEURI
-from genologics.entities import Artifact, Process, Sample
+from genologics.entities import Artifact
 from genologics.lims import Lims
 
 from cg_lims.get.ids import unique_list_of_ids

cg_lims/scripts/one_time_scripts/load_arnold_flowcells.py

@@ -5,7 +5,6 @@
 from genologics.lims import Lims
 import requests
 from requests import Response
-import json
 
 from cg_lims import options
 from cg_lims.EPPs.arnold.flow_cell import build_flow_cell_document

cg_lims/set/udfs.py

@@ -1,4 +1,5 @@
 import logging
+
 from typing import List, Tuple
 
 from genologics.entities import Artifact, Process

tests/EPPs/arnold/test_arnold_novaseq_standard.py

@@ -1,4 +1,4 @@
-from genologics.entities import Process, Processtype
+from genologics.entities import Process
 
 from cg_lims.EPPs.arnold.sequencing import build_step_documents
 from cg_lims.models.arnold.base_step import BaseStep

tests/EPPs/files/test_make_kapa_csv.py

@@ -2,7 +2,6 @@
 from pathlib import Path
 
 from genologics.entities import Artifact
-from genologics.entities import Sample
 
 import pytest
 

tests/EPPs/udf/calculate/test_calculate_average_size_and_set_qc.py

@@ -1,9 +1,8 @@
 import pytest
-from genologics.entities import Artifact, Process
+from genologics.entities import Process
 
 from cg_lims.EPPs.udf.calculate.calculate_average_size_and_set_qc import calculate_average_size, set_average_and_qc
-from cg_lims.exceptions import MissingUDFsError, MissingCgFieldError
-from cg_lims.set.udfs import copy_artifact_to_artifact
+from cg_lims.exceptions import MissingUDFsError
 from tests.conftest import server
 
 

tests/EPPs/udf/calculate/test_maf_calculate_volume.py

@@ -3,7 +3,6 @@
 
 import pytest
 from genologics.entities import Artifact
-from genologics.lims import Lims
 from pydantic.v1 import ValidationError
 
 from cg_lims.EPPs.udf.calculate.maf_calculate_volume import (

tests/EPPs/udf/copy/test_aggregate_qc_flags_and_copy_fields.py

@@ -1,8 +1,7 @@
 import pytest
-from genologics.entities import Artifact, Process
+from genologics.entities import Process
 
-from cg_lims.EPPs.udf.copy.aggregate_qc_flags_and_copy_fields import get_copy_tasks, copy_udfs
-from cg_lims.get.artifacts import get_artifacts
+from cg_lims.EPPs.udf.copy.aggregate_qc_flags_and_copy_fields import get_copy_tasks
 from cg_lims.exceptions import MissingUDFsError
 from tests.conftest import server
 

tests/EPPs/udf/copy/test_measurement_to_analyte.py

@@ -1,8 +1,8 @@
 import pytest
-from genologics.entities import Artifact, Process
+from genologics.entities import Process
 
 from cg_lims.EPPs.udf.copy.measurement_to_analyte import copy_udfs_to_all_analytes
-from cg_lims.get.artifacts import get_artifacts, get_latest_analyte
+from cg_lims.get.artifacts import get_artifacts
 from cg_lims.exceptions import MissingUDFsError
 from tests.conftest import server
 

tests/EPPs/udf/set/test_qc_to_sample.py

@@ -1,9 +1,8 @@
 import pytest
-from genologics.entities import Artifact, Process
+from genologics.entities import Process
 
-from cg_lims.exceptions import MissingUDFsError, MissingCgFieldError
+from cg_lims.exceptions import MissingUDFsError
 from cg_lims.EPPs.udf.copy.qc_to_sample import artifacts_to_sample
-from cg_lims.set.udfs import copy_artifact_to_artifact
 from tests.conftest import server
 
 from cg_lims.get.artifacts import get_artifacts

tests/EPPs/udf/set/test_set_method.py

@@ -9,7 +9,6 @@
 
 import responses
 import requests
-import logging
 
 
 @pytest.fixture()

tests/commands/test_base.py

@@ -1,6 +1,5 @@
 from pathlib import Path
 
-import pytest
 from click.testing import CliRunner
 
 from cg_lims.commands.base import cli

tests/conftest.py

@@ -1,5 +1,6 @@
-from typing import Dict, List, Optional
+from typing import Dict, List
 from unittest.mock import patch
+
 from genologics.lims import Lims
 from genologics.entities import Artifact, Process, Sample
 from pathlib import Path
@@ -16,7 +17,6 @@
 
 
 from limsmock.server import run_server
-from pydantic.v1 import BaseModel, Field
 
 from tests.fixtures.flowcell_document import FLOW_CELL_DOCUMENT